In the Wild Card Game, the Mets ran James Loney out to first base. In his very first at-bat, he snuffed out what could have been a rally by hitting into a double play on the first pitch he saw from Madison Bumgarner. In the seventh, he failed to field a groundball not hit too far from him that allowed Angel Pagan to reach on an infield single. That play effectively erased any chance that Noah Syndergaard could go back out for the eighth inning. Speaking of the eighth inning, with the Mets desperate for offense, Terry Collins pinch hit Eric Campbell for Loney.

Fact is, Loney shouldn’t have started that game. He didn’t have good numbers against left-handed pitching. He has been even worse against Bumgarner. However, he had to start with Lucas Duda not being ready to play, and with Wilmer Flores having suffered a season ending wrist injury.

All year long, Flores had demolished left-handed pitching. In 49 games against left-handed pitching, Flores hit .340/.383/.710 with 11 homers and 28 RBI. The Mets needed his bat in the lineup, and they needed him to play first base. However, he wasn’t available because of a crucial decision, or indecision, that was made on September 10th.

In that September 10th game, the Mets and Braves were tied 3-3 in the eighth inning, and Flores was standing on second base after a two out double. As we would soon see, with Flores’ speed, it was far from a guarantee that he would score from second on a base hit. Kelly Johnson would get a pinch-hit single. Flores “raced” around third, and he slid headfirst into home plate. In the ensuing collison, A.J. Pierzynski got him out – not just out at home plate, but also out for the season. Fact is, there is no reason why Flores wasn’t lifted there for a pinch runner. How did this happen?

Well, acccording to Collins, “We certainly had enough guys who could have ran for him, which we should have.” (Kevin Kernan, New York Post). Collins would go on to say, ““I was trying to get the pitching set up and get a pinch hitter in and got distracted, my faultI told [bench coach] Dickie [Scott], like I said, we were trying to get the pitching set up and get a pinch hitter, get somebody to hit for the pitcher who was coming up. I certainly should have had somebody ready to pinch run.”

Ultimately, Collins, being the manager and never one to make excuses, took responsibility for the failure to pinch run for Flores. However, it wasn’t just Collins’ mistake. It was also Bench Coach Dick Scott‘s mistake.

The bench coach’s job is more than just acting as a sounding board for the manager when seeking to make a move. The bench coach is also responsible for having a grasp of the matchups that are upcoming. They need to be aware of moves the team needs to be making in the next couple of innings. Overall, the bench coach needs to help prevent his manager, and ultimately his team, from making a gaffe that could cost them a game. During that confusion, Scott needed to remind Collins to get a pinch runner. He needed to be the clear head. If he did think of it, he needed to have a strong enough voice to get through to Collins.

What was simply astounding is the Mets almost repeated the mistake a week later. In the bottom of the seventh inning, the Mets were trailing the Minnesota Twins 1-0, and Ervin Santana was dealing. Loney was intentionally walked putting runners and first and second with no outs. Despite Loney representing the go-ahead run and being perhaps the slowest man in all of baseball, he was not pinch run for during Alejandro De Aza‘s at-bat. After De Aza walked, Loney was on second, again representing the go-ahead run. The Mets then sent Michael Conforto to bat for Jerry Blevins, and still Loney remained on second. After Conforto took the first pitch did the Mets send Ty Kelly out to second base to pinch run for Loney.

These weren’t isolated incidents. There are several other examples to pull from including the famous Collins’ rant about not knowing whether Jay Bruce or Brandon Nimmo is faster. If Collins didn’t know that, his bench coach sure should.

While Collins has his faults as a manager, there was never this sense of indecisiveness that we saw from the team this season. While Collins usually made head scratching moves, he usually had a justification for them. He would say that someone was swinging a hot bat, or the player has been a good player for them all season, or simply that he liked the matchup. He would never say there was distraction and confusion in the dugout. There was no reason for him to say it because Bob Geren was a good bench coach that helped not just his manager, but also his team. That calming presence and attention to detail was missed this year.

Geren’s work with catchers was also missed this year.

During Geren’s time in baseball, he has be renown for his work with catchers. If you recall, when Travis d’Arnaud had first come up with the Mets, there were many questions about his defense. In his first full season, he actually led the majors in passed balls, which is all the more alarming when you consider he spent a good amount of time in AAA. It wasn’t just the passed balls. During the season, d’Arnaud had trouble framing pitches, and his mechanics in all aspects behind the plate were out of whack – especially his throwing.

Working with Geren, d’Arnaud has built himself into one of the better catchers in baseball. He no longer has the issues with passed balls. He has shown the ability to call a good game. He is an exceptional pitch framer. There is probably no catcher better in the league in fielding a throw and getting the tag down without violating the plate blocking rules. In 2015, d’Aranud was actaully league average in throwing out base runners.

While d’Arnaud was good behind the plate this year, his mechanics throwing the ball took a step back. It could have been the shoulder injury, but it also could have been him missing the calming presence of Geren. Eventually, it became so much of an issue that Rene Rivera had to become Syndergaard’s personal catcher due to Syndergaard’s difficulties holding on base runners and d’Arnaud’s weak arm. There is no telling how all of this affected him mentally and whether this carried over to his offense.

So overall, the Mets truly missed Geren in the 2016 season, d’Arnaud especially. It was a rough first year for Scott as the bench coach. Despite it being a rough year, he will be returning to the staff next season. Although it has not been announced, he will presumably be returning to the same role. Hopefully, the growing pains are out of the way, and Scott will be a more effective bench coach in 2017.